arXiv subjects

Yue Ren

Publications and source records attributed to Yue Ren.

33 records · Page 2Linked to original sources

arXiv2020

Parallel Computation of tropical varieties, their positive part, and tropical Grassmannians

In this article, we present a massively parallel framework for computing tropicalizations of algebraic varieties which can make use of finite symmetries. We compute the tropical Grassmannian TGr$_0(3,8)$, and show that it refines the $15$-dimensional skeleton of the Dressian Dr$(3,8)$ with the exception of $23$ special cones for which we construct explicit obstructions to the realizability of their tropical linear spaces. Moreover, we propose algorithms for identifying maximal-dimensional tropical cones which belong to the positive tropicalization. These algorithms exploit symmetries of the tropical variety even though the positive tropicalization need not be symmetric. We compute the maximal-dimensional cones of the positive Grassmannian TGr$^+(3,8)$ and compare them to the cluster complex of the classical Grassmannian Gr$(3,8)$.

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arXiv2019

Detecting tropical defects of polynomial equations

We introduce the notion of tropical defects, certificates that a system of polynomial equations is not a tropical basis, and provide two algorithms for finding them in affine spaces of complementary dimension to the zero set. We use these techniques to solve open problems regarding del Pezzo surfaces of degree 3 and realizability of valuated gaussoids on 4 elements.

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arXiv2019

Computing zero-dimensional tropical varieties via projections

We present an algorithm for computing zero-dimensional tropical varieties using projections. Our main tools are fast unimodular transforms of lexicographical Gröbner bases. We prove that our algorithm requires only a polynomial number of arithmetic operations if given a Gröbner basis, and we demonstrate that our implementation compares favourably to other existing implementations. Applying it to the computation of general positive-dimensional tropical varieties, we argue that the complexity for calculating tropical links is dominated by the complexity of the Gröbner walk.

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arXiv2019

Cooperativity, Absolute Interaction, and Algebraic Optimization

We consider a measure of cooperativity based on the minimal absolute interaction required to generate an observed titration behavior. We describe the corresponding algebraic optimization problem and show how it can be solved using the nonlinear algebra tool \texttt{SCIP}. Moreover, we compute the minimal absolute interactions for various binding polynomials that describe the oxygen binding of various hemoglobins under different conditions. While calculated minimal absolute interactions are consistent with the expected outcome of the chemical modifications, it ranks the cooperativity of the molecules differently than the maximal Hill slope.

q-bio.BM↗

arXiv2019

Tropicalized quartics and canonical embeddings for tropical curves of genus 3

Brodsky, Joswig, Morrison and Sturmfels showed that not all abstract tropical curves of genus $3$ can be realized as a tropicalization of a quartic in the euclidean plane. In this article, we focus on the interior of the maximal cones in the moduli space and classify all curves which can be realized as a faithful tropicalization in a tropical plane. Reflecting the algebro-geometric world, we show that these are exactly those which are not realizably hyperelliptic. Our approach is constructive: For any not realizably hyperelliptic curve, we explicitly construct a realizable model of the tropical plane and a faithfully tropicalized quartic in it. These constructions rely on modifications resp. tropical refinements. Conversely, we prove that any realizably hyperelliptic curve cannot be embedded in such a fashion. For that, we rely on the theory of tropical divisors and embeddings from linear systems, and recent advances in the realizability of sections of the tropical canonical divisor.

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arXiv2018

Computing tropical points and tropical links

We present an algorithm for computing zero-dimensional tropical varieties based on triangular decomposition and Newton polygon methods. From it, we derive algorithms for computing points on and links of higher-dimensional tropical varieties, using intersections with affine hyperplanes to reduce the dimension to zero. We use the algorithms to show that the tropical Grassmannians $\mathcal G_{3,8}$ and $\mathcal G_{4,8}$ are not simplicial.

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arXiv2018

Real Space Sextics and their Tritangents

The intersection of a quadric and a cubic surface in 3-space is a canonical curve of genus 4. It has 120 complex tritangent planes. We present algorithms for computing real tritangents, and we study the associated discriminants. We focus on space sextics that arise from del Pezzo surfaces of degree one. Their numbers of planes that are tangent at three real points vary widely; both 0 and 120 are attained. This solves a problem suggested by Arnold Emch in 1928.

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arXiv2018

Tritangents and Their Space Sextics

Two classical results in algebraic geometry are that the branch curve of a del Pezzo surface of degree 1 can be embedded as a space sextic curve and that every space sextic curve has exactly 120 tritangents corresponding to its odd theta characteristics. In this paper we revisit both results from the computational perspective. Specifically, we give an algorithm to construct space sextic curves that arise from blowing up projective plane at eight points and provide algorithms to compute the 120 tritangents and their Steiner system of any space sextic. Furthermore, we develop efficient inverses to the aforementioned methods. We present an algorithm to either reconstruct the original eight points in the projective plane from a space sextic or certify that this is not possible. Moreover, we extend a construction of Lehavi which recovers a space sextic from its tritangents and Steiner system. All algorithms in this paper have been implemented in magma.

math.AG↗

arXiv2017

Decoupled molecules with binding polynomials of bidegree (n,2)

We present a result on the number of decoupled molecules for systems binding two different types of ligands. In the case of $n$ and $2$ binding sites respectively, we show that, generically, there are $2(n!)^{2}$ decoupled molecules with the same binding polynomial. For molecules with more binding sites for the second ligand, we provide computational results.

q-bio.BM↗

arXiv2017

Current Challenges in Developing Open Source Computer Algebra Systems

This note is based on the plenary talk given by the second author at MACIS 2015, the Sixth International Conference on Mathematical Aspects of Computer and Information Sciences. Motivated by some of the work done within the Priority Programme SPP 1489 of the German Research Council DFG, we discuss a number of current challenges in the development of Open Source computer algebra systems. The main focus is on algebraic geometry and the system Singular.

math.AG↗

arXiv2017

Computing GIT-fans with symmetry and the Mori chamber decomposition of $\bar{M}_{0,6}$

We propose an algorithm to compute the GIT-fan for torus actions on affine varieties with symmetries. The algorithm combines computational techniques from commutative algebra, convex geometry and group theory. We have implemented our algorithm in the Singular library gitfan.lib. Using our implementation, we compute the Mori chamber decomposition of the cone of movable divisors of $\bar{M}_{0,6}$.

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arXiv2016

Computing tropical varieties over fields with valuation

We show how tropical varieties of ideals I over a field K with non-trivial valuation can be traced back to tropical varieties of ideals in R[[t]][x] over some dense subring R in its ring of integers. Moreover, for homogeneous ideals, we present algorithms on how the latter can be computed in finite time, provided that generators are polynomial in t. While doing so, we also comment on the computation of the Groebner polytope structure and p-adic Groebner bases using our framework. All algorithms solely rely on existing standard basis techniques.

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arXiv2015

Gröbner Fans of x-homogeneous Ideals in R[[t]][x]

We generalise the notion of Gröbner fan to ideals in R[[t]][x_1,...,x_n] for certain classes of coefficient rings R and give a constructive proof that the Gröbner fan is a rational polyhedral fan. For this we introduce the notion of initially reduced standard bases and show how these can be computed in finite time. We deduce algorithms for computing the Gröbner fan, implemented in the computer algebra system Singular. The problem is motivated by the wish to compute tropical varieties over the p-adic numbers, which are the intersection of a subfan of a Gröbner fan as studied in this paper by some affine hyperplane, as shown in a forthcoming paper.

math.AC↗

arXiv2015

Standard Bases in mixed Power Series and Polynomial Rings over Rings

In this paper we study standard bases for submodules of a mixed power series and polynomial ring $R[[t_1,\ldots,t_m]][x_1,\ldots,x_n]^s$ respectively of their localization with respect to a $t$-local monomial ordering for a certain class of noetherian rings $R$. The main steps are to prove the existence of a division with remainder generalizing and combining the division theorems of Grauert--Hironaka and Mora and to generalize the Buchberger criterion. Everything else then translates naturally. Setting either $m=0$ or $n=0$ we get standard bases for polynomial rings respectively for power series rings over $R$ as a special case.

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arXiv2015

Mora's holy grail: Algorithms for computing in localizations at prime ideals

This article discusses a computational treatment of the localization A_L of an affine coordinate ring A at a prime ideal L and its associated graded ring Gr_a(A_L) with the means of standard basis techniques. Building on Mora's work, we present alternative proofs on two of the central statements and expand on the applications mentioned by Mora: resolutions of ideals, systems of parameters and Hilbert polynomials, as well as dimension and regularity of A_L. All algorithms are implemented in the library graal.lib for the computer algebra system Singular.

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